"""Refine MSA application."""
from ..apptools import DevelApp
__all__ = ['evol_filter']
APP = DevelApp('filter', 'filter an MSA using sequence labels')
APP.setExample(
"""Filter sequences in an MSA based on label data.
Following example will filter human sequences:
$ evol filter piwi_seed.slx HUMAN -e""", [])
APP.addArgument('msa',
help='MSA filename to be filtered')
APP.addArgument('word',
help='word to be compared to sequence label', nargs='+')
APP.addGroup('filter', 'filtering method (required)', True, True)
APP.addArgument('-s', '--startswith',
dest='startswith',
help='sequence label starts with given words',
action='store_true',
group='filter')
APP.addArgument('-e', '--endswith',
dest='endswith',
help='sequence label ends with given words',
action='store_true',
group='filter')
APP.addArgument('-c', '--contains',
dest='contains',
help='sequence label contains with given words',
action='store_true',
group='filter')
APP.addGroup('filter2', 'filter option')
APP.addArgument('-F', '--full-label',
dest='filter_full',
help='compare full label with word(s)',
action='store_true',
group='filter2')
APP.addGroup('output', 'output options')
APP.addArgument('-o', '--outname',
dest='outname',
help='output filename, default is msa filename with _refined suffix',
type=str,
metavar='STR',
group='output')
APP.addArgument('-f', '--format',
dest='format',
type=str,
metavar='STR',
help='output MSA file format, default is same as input',
group='output')
APP.addArgument('-z', '--compressed',
dest='compressed',
action='store_true',
help='gzip refined MSA output',
group='output')
[docs]def evol_filter(msa, *word, **kwargs):
import prody
from prody import MSAFile, writeMSA, LOGGER
from os.path import splitext
outname = kwargs.get('outname')
if outname is None:
outname, ext = splitext(msa)
if ext.lower() == '.gz':
outname, _ = splitext(msa)
outname += '_filtered' + ext
single = len(word) == 1
if single:
word = word[0]
if kwargs.get('startswith', False):
if single:
filter = lambda label, seq, word=word: label.startswith(word)
elif kwargs.get('endswith', False):
if single:
filter = lambda label, seq, word=word: label.endswith(word)
elif kwargs.get('contains', False):
if single:
filter = lambda label, seq, word=word: word in label
elif kwargs.get('equals', False):
if single:
filter = lambda label, seq, word=word: word == label
else:
filter = lambda label, seq, word=set(word): label in word
else:
raise TypeError('one of startswith, endswith, contains, or equals '
'must be specified')
msa = MSAFile(msa, filter=filter,
filter_full=kwargs.get('filter_full', False))
LOGGER.info('Filtered MSA is written in file: ' +
writeMSA(outname, msa, **kwargs))
APP.setFunction(evol_filter)
